Exploring the influence of vegetation carbon stocks over land-cover change and the relationship between land-cover change and net primary production (NPP) is of great practical importance for achieving China’s carbon neutrality target. Therefore, this paper analyses the spatio-temporal distribution of land-cover change and NPP change in Inner Mongolia from 2000 to 2020 and explores the vegetation carbon stock change caused by land-cover change, the relationship between land cover and NPP, and the relationship between land-cover change and NPP change. The results show that the main land-cover change in Inner Mongolia during 2000–2020 was the conversion from other land-cover types to grassland, with the conversion of bare land to grassland from 2000 to 2010 covering an area of 20,634.87 km2. During the period of 2000–2020, the high values of NPP were mainly located in northeastern Inner Mongolia, and the low values were mainly distributed in southwestern Inner Mongolia. The total carbon storage changes in vegetation affected by land-cover change during 2000–2010 and 2010–2020 were 10,736,986.11 t and 3,894,272.41 t. The mean values of NPP for different land covers were, in descending order, forest > cultivated land > wetland > grassland > artificial surfaces > shrubland > water bodies > bare land. Between 2000 and 2010, the change in land-cover type to water bodies was the main cause of the decrease in NPP, and the increase in NPP was mainly due to the conversion of other land-cover types to cultivated land, forest, and grassland. The implementation of appropriate conservation and management measures (e.g., the construction of forest and grass ecological protection), planting, and the protection of high-vegetation carbon storage plants and other means can improve the level of vegetation carbon sequestration and protect the ecological environment of Inner Mongolia.